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RESULTS SUMMARY - Based on abricate results
SAMPLEID PATHOGEN RESULT QC.STATUS
S-122-2 BVDv-Type-1 Negative OK
S-122-2 BVDv-Type-2 Negative OK
S-122-2 Bacillus licheniformis Negative OK
S-122-2 Bovine herpesvirus type-1 Positive OK
S-122-2 BVDv Negative OK
S-122-2 Campylobacter fetus Negative OK
S-122-2 Campylobacter fetus subsp. venerealis Negative OK
S-122-2 Campylobacter jejuni subsp. jejuni Negative OK
S-122-2 Chlamydia abortus Negative OK
S-122-2 Coxiella burnetii Positive OK
S-122-2 Internal amplification control Positive OK
S-122-2 Leptospira borgpetersenii serovar. Hardjo Negative OK
S-122-2 Leptospira interrogans serovar. Copenhageni Negative OK
S-122-2 Leptospira kirschneri Negative OK
S-122-2 Listeria monocytogenes Negative OK
S-122-2 Mycoplasma bovis Positive OK
S-122-2 Neospora caninum Negative OK
S-122-2 Sarcocystis bovini Negative OK
S-122-2 Sarcocystis cruzi Negative OK
S-122-2 Sarcocystis hirsuta Negative OK
S-122-2 Toxoplasma gondii Negative OK
S-122-2 Tritrichomonas foetus Negative OK
S-122-2 Trueperella pyogenes Positive OK
S-122-2 Ureaplasma diversum Negative OK
NO. OF MAPPED READS. Generated using minimap2 and samtools
AMPLICON MAPPED_READS
Coxiella_burnetti_Trans-1 20
IBR-gBN 18
IBR-gE 621
IC-EGFP 572
Trueperella_pyogenes_plo 400
Trueperella_pyogenes_sodA 109
Mbovis_PpSM5 139345
Mbovis_uvrC 13821
Consensus compared to reference database. Generated using abricate and custom database
SEQUENCE GENE %COVERAGE %IDENTITY DATABASE REFERENCE
S-122-2_Coxiella_burnetti_Trans-1 Transposon-like_element 100.00 98.91 Bovreproseq Coxiella_burnetii
S-122-2_IBR-gBN gB-glycoprotein_B 100.00 100.00 Bovreproseq Bovine_herpesvirus_type-1
S-122-2_IBR-gE gE-glycoprotein_E 100.00 100.00 Bovreproseq Bovine_herpesvirus_type-1
S-122-2_IC-EGFP IC-EGFP 100.00 100.00 Bovreproseq Internal_amplification_control
S-122-2_Mbovis_PpSM5 PPSM5 100.00 100.00 Bovreproseq Mycoplasma_bovis
S-122-2_Mbovis_uvrC uvrC-UV_excision_repair_gene 99.69 100.00 Bovreproseq Mycoplasma_bovis
S-122-2_Trueperella_pyogenes_plo PLO-Pyolysin 100.00 99.78 Bovreproseq Trueperella_pyogenes
S-122-2_Trueperella_pyogenes_sodA sodA-Superoxide_dismutase 100.00 100.00 Bovreproseq Trueperella_pyogenes 
>S-122-2_IC-EGFP_consensus
CAGCGTGTCCGGCGAGGGCGAGGGCGATGCCACCTACGGCAAGCTGACCCTGAAGTTCATCTGCACCACCGGCAAGCTGCCCGTGCCCTGGCCCACCCTCGTGACCACCCTGACCTACGGCGTGCAGTGCTTCAGCCGCTACCCCGACCACATGAAGCAGCACGACTTCTTCAAGTCCGCCATGCCCGAAGGCTACGTCCAGGAGCGCACCATCTTCTTCAAGGACGACGGCAACTACAAGACCCGCGCCGAGGTGAAGTTCGAGGGCGACACCCTGGTGAACCGCATCGAGCTGAAGGGCATCGACTTCAAGGAGGACGGCAACATCCTGGGGCACAAGCTGGAGTACAACTACAACAGCCACAACGTCTATATCATGGCCGACAAGCAGAAGAACGGCATCAAGGTGAACTTCAAGATCCGCCACAACATCGAGGACGGCAGCGTGCAGCTCGCCGACCACTACCAGCAGAACACCCCCATCGGCGACGGCCCCGTGCTGCTGCCCGA
>S-122-2_Mbovis_PpSM5_consensus
TTATCTCGGCTATACCTGAAAATGATGATGAGAGATTATTCTCAATTCAAGGAACCCCACCAGATATGGCAAACTTACCTATCGGTGACCCTTTTGCACCTAGAAATGACTTTGCCTTAGAAATTGACTATGAAAAAGAACCACCATTAATTGAAATTAATAGTCATCATAAAGCAGCAACGTGACTACTTCACCCTGATGCACCAAAAATACAAAGACCAAAAGAATTAGAACATAGACTAAAAAGTTTTAGAAAGGTATTTAAAGACGATGAAGAATAACGACAATAAAAAAGTCATTTTAGAAATTCAAGATCTTAAAAAGTACTTTTTAAATAACGGTAAGGTCAACAAAGCTGTTGATGGTGTGTCATTTAAATTACATGAAGG
>S-122-2_Trueperella_pyogenes_plo_consensus
TAGCTCGGGTCTTGTTCAGGATATCGGCATACTTAGCCTTGAACTCTGTGGAAAGATTGCCGAACTTAGCTTTGAACAGGCCGCTAAAAGCCGCTTGTACATCATTGGAAGTCGAGGTCGTTTCCAGCTTGACAAAAATCTGGCGTCCATAGCTGACCGACGAAATGTATCCTAGAGGATTCTTGTTATTGACTcCCCGATCTTTCAAATCCTGTGCGGTGACATTCGGGCCGAAAACGCTATGTGGAGATGTCGGTGTATCTACGCTAGCCGTGTAGTAAATCTGTTTGAAGGAAGCGATAGCCACCTGCCGTTCACGCTTATGAATTGCATCGAAGTCCACGTTGAGCTTGGCTGAGACCTTTTCAAATCCGAGGCCAAGCTTTGCCTCCAGTTGACGCTTTGACGTCACCATAGTCTCATCGTAAGAAATCTTTGCAGCATGGTCAGGATACTTGCTGTTGCGCTGAATCCAACCGTCGAGAAGGCCGTT
>S-122-2_IBR-gBN_consensus
TACATGTCGCCCTTTTACGGGCTGCGCGAGGGCGCGCACCGCGAGCACACCAGCTACTCGCCGGAGCGCTTCCAGCAGATCGAGGGCTACTACAAGCGCGACATGGCCACGGGCCGGCGCCTCAAGGAGCCGGTCTCGCGGAACTTTTTGCGTACACAGCACGTGACGGTAGCCTGGGACTGGGTGCCCAAGCGCAAAAACGTGTGCTCGCTGGCCAAGTGGCGCGAGGCGGACGAAATGCTGCGAGACGAGAGCCGCGGGAACTTCCGCTTCACGGCCCGCTCGCTCTCGGCGACCTTTGTGAGCGACAGCCACACCTTCGCGTTGCAGAATGTGCCGCTGAGC
>S-122-2_IBR-gE_consensus
CACGGCGCGCGCTGGCGCGCCCGTCtTTCTCCCAGGGCCCGCGGCGCGCCCGGACGTGCGCGCCGTTCGCGGCTGGAGCGTCCTCGCGGGCGCCTGCTCGCCGCCCGTGCCGGAGCCCGTCTGCCTCGACGACCGCGAGTGCTTCACCGACGTGGCCCTGGACGCGGCCTGCCTGCGAACCGCCCGCGTGGCCCCGCTGGCCATCGCGGAGCTCGCCGAGCGGCC
>S-122-2_Trueperella_pyogenes_sodA_consensus
CAACTGGCACGTTGGCCTGCTGGTCGAAAAGCTGGAACGTGATCAAGCCGCCCGAAATCGTGTCGTAGGCGAGCACGGCCCAGCCTGAGCCCTGGATGCCGGTAGCCACCGCGGTGAACTGCTTCTTGAAATCTTCGAATGATCCGAAAGC
>S-122-2_Coxiella_burnetti_Trans-1_consensus
TTAAGGTGGGCTGCGTGGTGATGGAAGCGTGTGGAGGAGCGAACCATTGGTATCGGACGTTTATGGGGATGGGTATCYCAACGCAGTTGATCAGTCCGCAGCACGTCAAACCGTATGTCAAAAGTAACAAGAATGATCGTAACGATGCGCAGGCGATAGCTGAAGCGGCTTCCCGCGCCTCGATGCGGTTTGTGCGGGGTAAAACGGTGGAACAACAAGACGTTCAAGCGCTGTTAAAGATACGCGATCGTTTAGTCAAAAGCCGCACGGCGCTGATCAATGAGATTCGGGGGTTGTTGCAAGAATACGGACTCACGATGGCgGCGTGGTGCCAAGCGATTTTATGAAGAGCTCCCGTTGATTTTAGCGAGCGAAGCGGTGGGATTAACACCGCGGATGAAACGGGTGTTGAATTGTTTGTATACCGAATTGTTGAACCGGGACGAAGCNATTGGTGATTACGAGGAGGAATTAAAAGCGGTGGCAAAAGCCAATGAGGATTGTCAACGGGTACAGAGCATCCCGGGGGTGGGTTATTTAACGGCGCTGTCGGTTTATGCGAGCGTGGGTGACATTCATCAATTTCATCGTTCCCGGCAGTTGTCGGCGTTTATTGGGTTGGTCCMTCGACAACATTCGAGKG
>S-122-2_Mbovis_uvrC_consensus
TATACTAATGGAATTAAAAACAAAAGCTTATATAGAAAATTTAATTTAGAAGCTTTAAATGAGCGCAGTGCTGATGTTGAATATATTAAGCAATCAATTTCTAAATTTTTTAGTAGCAACAAAAACACTAAAGATTATGACTTAGTTATAGCTGATGGCGGTATACAACAAGTTAATGAAGCTAAAAAAACGCTTAAAACGCTTAATATAAACATCCCTGTTATTGGATTAGTAAAAAATGAGTTTCACAAAACCAAAGCCTTAATTGACCTAGATATGAATGAAATTCATATTAATGACTTAGAACTATACAACTACTTAGTTC

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RESULTS SUMMARY - Based on abricate results
SAMPLEID PATHOGEN RESULT QC.STATUS
S-123-2 BVDv-Type-1 Negative OK
S-123-2 BVDv-Type-2 Positive OK
S-123-2 Bacillus licheniformis Negative OK
S-123-2 Bovine herpesvirus type-1 Positive OK
S-123-2 BVDv Positive OK
S-123-2 Campylobacter fetus Negative OK
S-123-2 Campylobacter fetus subsp. venerealis Negative OK
S-123-2 Campylobacter jejuni subsp. jejuni Negative OK
S-123-2 Chlamydia abortus Negative OK
S-123-2 Coxiella burnetii Negative OK
S-123-2 Internal amplification control Positive OK
S-123-2 Leptospira borgpetersenii serovar. Hardjo Negative OK
S-123-2 Leptospira interrogans serovar. Copenhageni Negative OK
S-123-2 Leptospira kirschneri Negative OK
S-123-2 Listeria monocytogenes Negative OK
S-123-2 Mycoplasma bovis Positive OK
S-123-2 Neospora caninum Negative OK
S-123-2 Sarcocystis bovini Negative OK
S-123-2 Sarcocystis cruzi Negative OK
S-123-2 Sarcocystis hirsuta Negative OK
S-123-2 Toxoplasma gondii Negative OK
S-123-2 Tritrichomonas foetus Negative OK
S-123-2 Trueperella pyogenes Positive OK
S-123-2 Ureaplasma diversum Positive OK
NO. OF MAPPED READS. Generated using minimap2 and samtools
AMPLICON MAPPED_READS
BVDv-2_5’UTR 509
IBR-gBN 241
IBR-gE 4119
IC-EGFP 391
Ureaplasmadiversum-16SrRNA 23182
Ureaplasmaspp_UGP 13098
Trueperella_pyogenes_plo 10
Trueperella_pyogenes_sodA 22
Mbovis_PpSM5 88388
Mbovis_uvrC 6905
Consensus compared to reference database. Generated using abricate and custom database
SEQUENCE GENE %COVERAGE %IDENTITY DATABASE REFERENCE
S-123-2_BVDv-2_5’UTR 5’UTR 100.00 99.18 Bovreproseq BVDv-Type-2
S-123-2_IBR-gBN gB-glycoprotein_B 100.00 100.00 Bovreproseq Bovine_herpesvirus_type-1
S-123-2_IBR-gE gE-glycoprotein_E 100.00 100.00 Bovreproseq Bovine_herpesvirus_type-1
S-123-2_IC-EGFP IC-EGFP 100.00 100.00 Bovreproseq Internal_amplification_control
S-123-2_Mbovis_PpSM5 PPSM5 100.00 100.00 Bovreproseq Mycoplasma_bovis
S-123-2_Mbovis_uvrC uvrC-UV_excision_repair_gene 99.69 100.00 Bovreproseq Mycoplasma_bovis
S-123-2_Trueperella_pyogenes_plo PLO-Pyolysin 100.00 99.78 Bovreproseq Trueperella_pyogenes
S-123-2_Trueperella_pyogenes_sodA sodA-Superoxide_dismutase 100.00 100.00 Bovreproseq Trueperella_pyogenes
S-123-2_Ureaplasmadiversum-16SrRNA UD-16SrRNA 100.00 100.00 Bovreproseq Ureaplasma_diversum
S-123-2_Ureaplasmaspp_UGP UGP-16SrRNA 100.00 99.83 Bovreproseq Ureaplasma_diversum 
>S-123-2_IC-EGFP_consensus
CAGCGTGTCCGGCGAGGGCGAGGGCGATGCCACCTACGGCAAGCTGACCCTGAAGTTCATCTGCACCACCGGCAAGCTGCCCGTGCCCTGGCCCACCCTCGTGACCACCCTGACCTACGGCGTGCAGTGCTTCAGCCGCTACCCCGACCACATGAAGCAGCACGACTTCTTCAAGTCCGCCATGCCCGAAGGCTACGTCCAGGAGCGCACCATCTTCTTCAAGGACGACGGCAACTACAAGACCCGCGCCGAGGTGAAGTTCGAGGGCGACACCCTGGTGAACCGCATCGAGCTGAAGGGCATCGACTTCAAGGAGGACGGCAACATCCTGGGGCACAAGCTGGAGTACAACTACAACAGCCACAACGTCTATATCATGGCCGACAAGCAGAAGAACGGCATCAAGGTGAACTTCAAGATCCGCCACAACATCGAGGACGGCAGCGTGCAGCTCGCCGACCACTACCAGCAGAACACCCCCATCGGCGACGGCCCCGTGCTGCTGCCCGA
>S-123-2_Ureaplasmadiversum-16SrRNA_consensus
TCGGTGTTGTAGCTAACGCATTAAATGATGTGCCTGGGTAGTACATTCGCAAGAATGAAACTCAAACGGAATTGACGGGGACCCGCACAAGTGGTGGAGCATGTTGCTTAATTTGACAATACACGTAGAACCTTACCTAGGTTTGACATCTATTGCAATGCTATAGAAATATAGCGGAGGTTAACAATATGACAGGTGGTGCATGGTTGTCGTCAGCTCGTGTCGTGAGATGTTGGGTTAAGTCCCGCAACGAGCGCAACCCCTTTCGC
>S-123-2_Mbovis_PpSM5_consensus
TTATCTCGGCTATACCTGAAAATGATGATGAGAGATTATTCTCAATTCAAGGAACCCCACCAGATATGGCAAACTTACCTATCGGTGACCCTTTTGCACCTAGAAATGACTTTGCCTTAGAAATTGACTATGAAAAAGAACCACCATTAATTGAAATTAATAGTCATCATAAAGCAGCAACGTGACTACTTCACCCTGATGCACCAAAAATACAAAGACCAAAAGAATTAGAACATAGACTAAAAAGTTTTAGAAAGGTATTTAAAGACGATGAAGAATAACGACAATAAAAAAGTCATTTTAGAAATTCAAGATCTTAAAAAGTACTTTTTAAATAACGGTAAGGTCAACAAAGCTGTTGATGGTGTGTCATTTAAATTACATGAAGG
>S-123-2_Trueperella_pyogenes_plo_consensus
TAGCTCGGGTCTTGTTCAGGATATCGGCATACTTAGCCTTGAACTCTGTGGAAAGATTGCCGAACTTAGCTTTGAACAGGCCGCTAAAAGCCGCTTGTACATCATTGGAAGTCGAGGTCGTTTCCAGCTTGACAAAAATCTGGCGTCCATAGCTGACCGACGAAATGTATCCTAGAGGATTCTTGTTATTGACTCCCCGATCTTTCAAATCCTGTGCGGTGACATTCGGGCCGAAAACGCTATGTGGAGATGTCGGTGTATCTACGCTAGCCGTGTAGTAAATCTGTTTGAAGGAAGCGATAGCCACCTGCCGTTCACGCTTATGAATTGCATCGAAGTCCACGTTGAGCTTGGCTGAGACCTTTTCAAATCCGAGGCCAAGCTTTGCCTCCAGTTGACGCTTTGACGTCACCATAGTCTCATCGTAAGAAATCTTTGCAGCATGGTCAGGATACTTGCTGTTGCGCTGAATCCAACCGTCGAGAAGGCCGTT
>S-123-2_Trueperella_pyogenes_sodA_consensus
CAACTGGCACGTTGGCCTGCTGGTCGAAAAGCTGGAACGTGATCAAGCCGCCCGAAATCGTGTCGTAGGCGAGCACGGCCCAGCCTGAGCCCTGGATGCCGGTAGCCACCGCGGTGAACTGCTTCTTGAAATCTTCGAATGATCCGAAAGC
>S-123-2_IBR-gE_consensus
CACGGCGCGCGCTGGCGCGCCCGTCTTTCTCCCAGGGCCCGCGGCGCGCCCGGACGTGCGCGCCGTTCGCGGCTGGAGCGTCCTCGCGGGCGCCTGCTCGCCGCCCGTGCCGGAGCCCGTCTGCCTCGACGACCGCGAGTGCTTCACCGACGTGGCCCTGGACGCGGCCTGCCTGCGAACCGCCCGCGTGGCCCCGCTGGCCATCGCGGAGCTCGCCGAGCGGCC
>S-123-2_Mbovis_uvrC_consensus
TATACTAATGGAATTAAAAACAAAAGCTTATATAGAAAATTTAATTTAGAAGCTTTAAATGAGCGCAGTGCTGATGTTGAATATATTAAGCAATCAATTTCTAAATTTTTTAGTAGCAACAAAAACACTAAAGATTATGACTTAGTTATAGCTGATGGCGGTATACAACAAGTTAATGAAGCTAAAAAAACGCTTAAAACGCTTAATATAAACATCCCTGTTATTGGATTAGTAAAAAATGAGTTTCACAAAACCAAAGCCTTAATTGACCTAGATATGAATGAAATTCATATTAATGACTTAGAACTATACAACTACTTAGTTC
>S-123-2_BVDv-2_5'UTR_consensus
AAAAGGAGGGGACTAGCGGTAGCAGTGAGTTCATTGGATGGCCGAATCCCTGAGTACAGGGAAGTCGTCAGTGGTTCGACACTCCATCAACCGAGGAGTCTCGAGATGCCATGTGGACGAGGGCATGCCCACGGCACATCTTAACCTATGCGGGGGTTGCATGGGTGAAAGCACCATTCGTGGTGTTATGGACACAGCCTGATAGGGTGTAGCAGAGACCTGCTATTCCGCTAGTAAAAACTCTG
>S-123-2_IBR-gBN_consensus
TACATGTCGCCCTTTTACGGGCTGCGCGAGGGCGCGCACCGCGAGCACACCAGCTACTCGCCGGAGCGCTTCCAGCAGATCGAGGGCTACTACAAGCGCGACATGGCCACGGGCCGGCGCCTCAAGGAGCCGGTCTCGCGGAACTTTTTGCGTACACAGCACGTGACGGTAGCCTGGGACTGGGTGCCCAAGCGCAAAAACGTGTGCTCGCTGGCCAAGTGGCGCGAGGCGGACGAAATGCTGCGAGACGAGAGCCGCGGGAACTTCCGCTTCACGGCCCGCTCGCTCTCGGCGACCTTTGTGAGCGACAGCCACACCTTCGCGTTGCAGAATGTGCCGCTGAGC
>S-123-2_Ureaplasmaspp_UGP_consensus
AGATAGTTGGTGAGGTAACGGCTCACCAAGTCATTGACGCGTAGCTGTACTGAGAGGTAGAACAGCCACAATGGGACTGAGACACGGCCCATACTCCTACGGGAGGCAGCAGTAGGGAATTTTTCACAATGGGCGAAAGCCTTATGAAGCAATGCCGCGTGAACGATGAAGGTCTATAAGATTGTAAAGTTCTTTTATTTGGGAAGAACCACTAAAATAGGAAATGATTTTAGTTTGACTGTACCATTTGAATAAGTATCGGCTAACTATGTGCCAGCAGCCGCGGTAATACATAGGATGCAAGCGTTATCCGGATTTACTGGGCGTAAAACGAGCGCAGGCGGATTTGTAAGTTTGGTATGAAATCTAGATGCTTAACGTCTAGCTGTATCAAAAACTACGAATCTAGAGTGTAGCAGAGAGTTGGGGAACTCCATGTGGAGCGGTAAAATGCGTAGATATATGGAAGAACACCGGTGGCGAAGGCGCCAACTTGGACTATTACTGACGCTTAGGCTCGAAAGTGTGGGGAGCAAATAGGATTAGATACCCTAGTAGTCCACACCGTAAACGATCATCATTAAATGTCGGCTCGCTTATGA

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RESULTS SUMMARY - Based on abricate results
SAMPLEID PATHOGEN RESULT QC.STATUS
S-175-4 BVDv-Type-1 Negative Check for PCR inhibition
S-175-4 BVDv-Type-2 Negative Check for PCR inhibition
S-175-4 Bacillus licheniformis Negative Check for PCR inhibition
S-175-4 Bovine herpesvirus type-1 Negative Check for PCR inhibition
S-175-4 BVDv Negative Check for PCR inhibition
S-175-4 Campylobacter fetus Negative Check for PCR inhibition
S-175-4 Campylobacter fetus subsp. venerealis Negative Check for PCR inhibition
S-175-4 Campylobacter jejuni subsp. jejuni Negative Check for PCR inhibition
S-175-4 Chlamydia abortus Negative Check for PCR inhibition
S-175-4 Coxiella burnetii Negative Check for PCR inhibition
S-175-4 Internal amplification control Negative Check for PCR inhibition
S-175-4 Leptospira borgpetersenii serovar. Hardjo Negative Check for PCR inhibition
S-175-4 Leptospira interrogans serovar. Copenhageni Negative Check for PCR inhibition
S-175-4 Leptospira kirschneri Negative Check for PCR inhibition
S-175-4 Listeria monocytogenes Negative Check for PCR inhibition
S-175-4 Mycoplasma bovis Negative Check for PCR inhibition
S-175-4 Neospora caninum Negative Check for PCR inhibition
S-175-4 Sarcocystis bovini Negative Check for PCR inhibition
S-175-4 Sarcocystis cruzi Negative Check for PCR inhibition
S-175-4 Sarcocystis hirsuta Negative Check for PCR inhibition
S-175-4 Toxoplasma gondii Negative Check for PCR inhibition
S-175-4 Tritrichomonas foetus Negative Check for PCR inhibition
S-175-4 Trueperella pyogenes Positive Check for PCR inhibition
S-175-4 Ureaplasma diversum Negative Check for PCR inhibition
NO. OF MAPPED READS. Generated using minimap2 and samtools
AMPLICON MAPPED_READS
Trueperella_pyogenes_sodA 689
Consensus compared to reference database. Generated using abricate and custom database
SEQUENCE GENE %COVERAGE %IDENTITY DATABASE REFERENCE
S-175-4_Trueperella_pyogenes_sodA sodA-Superoxide_dismutase 100 99.34 Bovreproseq Trueperella_pyogenes 
>S-175-4_Trueperella_pyogenes_sodA_consensus
CAACTGGCACGTTGGCCTGCTGGTCGAAAAGCTGGAACGTGATCAAGCCGCCCGAAATCGTGTCGTAGGCGAGCACGGCCCAGCCTGAGCCCTGGATGCCGGTAGCCACCGCGGTGAACTGCCTCTTGAAATCTTCGAATGATCCGAAAGC

Download FASTA file

RESULTS SUMMARY - Based on abricate results
SAMPLEID PATHOGEN RESULT QC.STATUS
S-266-3 BVDv-Type-1 Negative OK
S-266-3 BVDv-Type-2 Positive OK
S-266-3 Bacillus licheniformis Negative OK
S-266-3 Bovine herpesvirus type-1 Negative OK
S-266-3 BVDv Positive OK
S-266-3 Campylobacter fetus Negative OK
S-266-3 Campylobacter fetus subsp. venerealis Negative OK
S-266-3 Campylobacter jejuni subsp. jejuni Negative OK
S-266-3 Chlamydia abortus Negative OK
S-266-3 Coxiella burnetii Negative OK
S-266-3 Internal amplification control Positive OK
S-266-3 Leptospira borgpetersenii serovar. Hardjo Negative OK
S-266-3 Leptospira interrogans serovar. Copenhageni Negative OK
S-266-3 Leptospira kirschneri Negative OK
S-266-3 Listeria monocytogenes Negative OK
S-266-3 Mycoplasma bovis Positive OK
S-266-3 Neospora caninum Negative OK
S-266-3 Sarcocystis bovini Negative OK
S-266-3 Sarcocystis cruzi Negative OK
S-266-3 Sarcocystis hirsuta Negative OK
S-266-3 Toxoplasma gondii Negative OK
S-266-3 Tritrichomonas foetus Negative OK
S-266-3 Trueperella pyogenes Negative OK
S-266-3 Ureaplasma diversum Positive OK
NO. OF MAPPED READS. Generated using minimap2 and samtools
AMPLICON MAPPED_READS
BVDv-2_5’UTR 99
IC-EGFP 815
Ureaplasmadiversum-16SrRNA 29912
Ureaplasmaspp_UGP 26984
Mbovis_PpSM5 13602
Mbovis_uvrC 229
Consensus compared to reference database. Generated using abricate and custom database
SEQUENCE GENE %COVERAGE %IDENTITY DATABASE REFERENCE
S-266-3_BVDv-2_5’UTR 5’UTR 100.00 94.69 Bovreproseq BVDv-Type-2
S-266-3_IC-EGFP IC-EGFP 100.00 100.00 Bovreproseq Internal_amplification_control
S-266-3_Mbovis_PpSM5 PPSM5 100.00 99.23 Bovreproseq Mycoplasma_bovis
S-266-3_Mbovis_uvrC uvrC-UV_excision_repair_gene 99.69 97.84 Bovreproseq Mycoplasma_bovis
S-266-3_Ureaplasmadiversum-16SrRNA UD-16SrRNA 100.00 100.00 Bovreproseq Ureaplasma_diversum
S-266-3_Ureaplasmaspp_UGP UGP-16SrRNA 100.00 99.83 Bovreproseq Ureaplasma_diversum 
>S-266-3_IC-EGFP_consensus
CAGCGTGTCCGGCGAGGGCGAGGGCGATGCCACCTACGGCAAGCTGACCCTGAAGTTCATCTGCACCACCGGCAAGCTGCCCGTGCCCTGGCCCACCCTCGTGACCACCCTGACCTACGGCGTGCAGTGCTTCAGCCGCTACCCCGACCACATGAAGCAGCACGACTTCTTCAAGTCCGCCATGCCCGAAGGCTACGTCCAGGAGCGCACCATCTTCTTCAAGGACGACGGCAACTACAAGACCCGCGCCGAGGTGAAGTTCGAGGGCGACACCCTGGTGAACCGCATCGAGCTGAAGGGCATCGACTTCAAGGAGGACGGCAACATCCTGGGGCACAAGCTGGAGTACAACTACAACAGCCACAACGTCTATATCATGGCCGACAAGCAGAAGAACGGCATCAAGGTGAACTTCAAGATCCGCCACAACATCGAGGACGGCAGCGTGCAGCTCGCCGACCACTACCAGCAGAACACCCCCATCGGCGACGGCCCCGTGCTGCTGCCCGA
>S-266-3_Mbovis_PpSM5_consensus
TTATCTCGGCTATACCTGAAAATGATGATGAGAGATTATTCTCAATTCAAGGAACCCCACCAGATATGGCAAACTTACCTATCGGTGACCCTTTTGCGCCTAGAAATGACTTTGCTTTAGAAATTGACTATGAAAAAGAACCACCATTAATTGAAATTAATAGTCATCATAAAGCAGCAACGTGACTACTTCACCCTGATGCACCAAAAATACAAAGACCAAAAGAATTAGAACATAGACTAAAAAGTTTTAGAAAGGTATTTAAAGACGATGAAGAATAACGACAATAAAAAAGTCATTTTAGAAATTCAAGATCTTAAAAAGTACTTTTTAAACAACGGTAAGGTCAACAAAGCTGTTGATGGTGTGTCATTTAAATTACATGAAGG
>S-266-3_Ureaplasmadiversum-16SrRNA_consensus
TCGGTGTTGTAGCTAACGCATTAAATGATGTGCCTGGGTAGTACATTCGCAAGAATGAAACTCAAACGGAATTGACGGGGACCCGCACAAGTGGTGGAGCATGTTGCTTAATTTGACAATACACGTAGAACCTTACCTAGGTTTGACATCTATTGCAATGCTATAGAAATATAGCGGAGGTTAACAATATGACAGGTGGTGCATGGTTGTCGTCAGCTCGTGTCGTGAGATGTTGGGTTAAGTCCCGCAACGAGCGCAACCCCTTTCGC
>S-266-3_Mbovis_uvrC_consensus
TATACTAATGGAATTAAAAACAAAAGCTTATATAGAAAATTTAATTTAGAAGCTTTAAATGAGCGCAGTGCTGATGTTGAATATATTAAGCAATCAATTTCTAAATTTTTTAGTAGCAACAAAAACACTAAAGATTATGACTTAGTTATAGCTGATGGTGGTGTACAACAAGTTAATGAAGCTAAAAAAACGCTTAAAACACTTAATATAAACATCCCTGTTATTGGATTAGTAAAAAATGAGTTTCACAAAACTAAAGCCTTAATTGACCTAGATATGAATGAAATTCACATTTCTGACTTAGAACTATACAACTACTTAGTTC
>S-266-3_BVDv-2_5'UTR_consensus
AAAAATAGGGGACTAGCGGTAGCAGTGAGTTCATTGGATGGCCGAACCCCTGAGTACAGGGGAGTCGTCAATGGTTCGACACTCCATTGGTTGAGGAGTCTCGAGATGCCATGTGGACGAGGGCATGCCCACGGCACATCTTAACCCATGCGGGGGTTGCATGGGTGAAAGCGCTATTCATGGCGTTATGGACACAGCCTGATAGGGTGTAGCAGAGACCTGCTATTCCGCTAGTAAAAACTCTG
>S-266-3_Ureaplasmaspp_UGP_consensus
AGATAGTTGGTGAGGTAACGGCTCACCAAGTCATTGACGCGTAGCTGTACTGAGAGGTAGAACAGCCACAATGGGACTGAGACACGGCCCATACTCCTACGGGAGGCAGCAGTAGGGAATTTTTCACAATGGGCGAAAGCCTTATGAAGCAATGCCGCGTGAACGATGAAGGTCTATAAGATTGTAAAGTTCTTTTATTTGGGAAGAACCACTAAAATAGGAAATGATTTTAGTTTGACTGTACCATTTGAATAAGTATCGGCTAACTATGTGCCAGCAGCCGCGGTAATACATAGGATGCAAGCGTTATCCGGATTTACTGGGCGTAAAACGAGCGCAGGCGGATTTGTAAGTTTGGTATGAAATCTAGATGCTTAACGTCTAGCTGTATCAAAAACTACGAATCTAGAGTGTAGCAGAGAGTTGGGGAACTCCATGTGGAGCGGTAAAATGCGTAGATATATGGAAGAACACCGGTGGCGAAGGCGCCAACTTGGACTATTACTGACGCTTAGGCTCGAAAGTGTGGGGAGCAAATAGGATTAGATACCCTAGTAGTCCACACCGTAAACGATCATCATTAAATGTCGGCTCGCTTATGA

Download FASTA file

RESULTS SUMMARY - Based on abricate results
SAMPLEID PATHOGEN RESULT QC.STATUS
S-363 BVDv-Type-1 Negative OK
S-363 BVDv-Type-2 Negative OK
S-363 Bacillus licheniformis Negative OK
S-363 Bovine herpesvirus type-1 Negative OK
S-363 BVDv Negative OK
S-363 Campylobacter fetus Negative OK
S-363 Campylobacter fetus subsp. venerealis Negative OK
S-363 Campylobacter jejuni subsp. jejuni Negative OK
S-363 Chlamydia abortus Negative OK
S-363 Coxiella burnetii Negative OK
S-363 Internal amplification control Positive OK
S-363 Leptospira borgpetersenii serovar. Hardjo Negative OK
S-363 Leptospira interrogans serovar. Copenhageni Negative OK
S-363 Leptospira kirschneri Negative OK
S-363 Listeria monocytogenes Negative OK
S-363 Mycoplasma bovis Negative OK
S-363 Neospora caninum Negative OK
S-363 Sarcocystis bovini Negative OK
S-363 Sarcocystis cruzi Positive OK
S-363 Sarcocystis hirsuta Negative OK
S-363 Toxoplasma gondii Negative OK
S-363 Tritrichomonas foetus Negative OK
S-363 Trueperella pyogenes Negative OK
S-363 Ureaplasma diversum Negative OK
NO. OF MAPPED READS. Generated using minimap2 and samtools
AMPLICON MAPPED_READS
IC-EGFP 210690
Coccidia_Sarcocystiscruzi 661
Consensus compared to reference database. Generated using abricate and custom database
SEQUENCE GENE %COVERAGE %IDENTITY DATABASE REFERENCE
S-363_Coccidia_Sarcocystiscruzi Coccidia-18SrRNA 83.27 92.37 Bovreproseq Sarcocystis_cruzi
S-363_IC-EGFP IC-EGFP 100.00 100.00 Bovreproseq Internal_amplification_control 
>S-363_IC-EGFP_consensus
CAGCGTGTCCGGCGAGGGCGAGGGCGATGCCACCTACGGCAAGCTGACCCTGAAGTTCATCTGCACCACCGGCAAGCTGCCCGTGCCCTGGCCCACCCTCGTGACCACCCTGACCTACGGCGTGCAGTGCTTCAGCCGCTACCCCGACCACATGAAGCAGCACGACTTCTTCAAGTCCGCCATGCCCGAAGGCTACGTCCAGGAGCGCACCATCTTCTTCAAGGACGACGGCAACTACAAGACCCGCGCCGAGGTGAAGTTCGAGGGCGACACCCTGGTGAACCGCATCGAGCTGAAGGGCATCGACTTCAAGGAGGACGGCAACATCCTGGGGCACAAGCTGGAGTACAACTACAACAGCCACAACGTCTATATCATGGCCGACAAGCAGAAGAACGGCATCAAGGTGAACTTCAAGATCCGCCACAACATCGAGGACGGCAGCGTGCAGCTCGCCGACCACTACCAGCAGAACACCCCCATCGGCGACGGCCCCGTGCTGCTGCCCGA
>S-363_Coccidia_Sarcocystiscruzi_consensus
TGCACTTGATGAATTCTGGCATCTATGTCCCAATAgtATGTGATGGTGTAtaTATACCCTGTGtataTAYtAttatMCCATCTATATTGGGATAATACCGTTACTTTGAGAAAATTAGAGTGTTTGAAGCAGGCTAATTGCCTTGAATACTGCAGCATGGAATAACAATATAGGATTTCGGTTCTATTTTGTTGGTTTCTAGGACTGAAATAATGATTAATAGGGACAGTTGGGGGCATTCGTATTTAA

Download FASTA file

RESULTS SUMMARY - Based on abricate results
SAMPLEID PATHOGEN RESULT QC.STATUS
S-443 BVDv-Type-1 Negative OK
S-443 BVDv-Type-2 Negative OK
S-443 Bacillus licheniformis Negative OK
S-443 Bovine herpesvirus type-1 Negative OK
S-443 BVDv Negative OK
S-443 Campylobacter fetus Negative OK
S-443 Campylobacter fetus subsp. venerealis Negative OK
S-443 Campylobacter jejuni subsp. jejuni Negative OK
S-443 Chlamydia abortus Negative OK
S-443 Coxiella burnetii Negative OK
S-443 Internal amplification control Positive OK
S-443 Leptospira borgpetersenii serovar. Hardjo Negative OK
S-443 Leptospira interrogans serovar. Copenhageni Negative OK
S-443 Leptospira kirschneri Negative OK
S-443 Listeria monocytogenes Negative OK
S-443 Mycoplasma bovis Negative OK
S-443 Neospora caninum Negative OK
S-443 Sarcocystis bovini Negative OK
S-443 Sarcocystis cruzi Positive OK
S-443 Sarcocystis hirsuta Negative OK
S-443 Toxoplasma gondii Negative OK
S-443 Tritrichomonas foetus Negative OK
S-443 Trueperella pyogenes Negative OK
S-443 Ureaplasma diversum Negative OK
NO. OF MAPPED READS. Generated using minimap2 and samtools
AMPLICON MAPPED_READS
IC-EGFP 125536
Coccidia_Sarcocystiscruzi 2013
Consensus compared to reference database. Generated using abricate and custom database
SEQUENCE GENE %COVERAGE %IDENTITY DATABASE REFERENCE
S-443_Coccidia_Sarcocystiscruzi Coccidia-18SrRNA 100 85.06 Bovreproseq Sarcocystis_cruzi
S-443_IC-EGFP IC-EGFP 100 100.00 Bovreproseq Internal_amplification_control 
>S-443_IC-EGFP_consensus
CAGCGTGTCCGGCGAGGGCGAGGGCGATGCCACCTACGGCAAGCTGACCCTGAAGTTCATCTGCACCACCGGCAAGCTGCCCGTGCCCTGGCCCACCCTCGTGACCACCCTGACCTACGGCGTGCAGTGCTTCAGCCGCTACCCCGACCACATGAAGCAGCACGACTTCTTCAAGTCCGCCATGCCCGAAGGCTACGTCCAGGAGCGCACCATCTTCTTCAAGGACGACGGCAACTACAAGACCCGCGCCGAGGTGAAGTTCGAGGGCGACACCCTGGTGAACCGCATCGAGCTGAAGGGCATCGACTTCAAGGAGGACGGCAACATCCTGGGGCACAAGCTGGAGTACAACTACAACAGCCACAACGTCTATATCATGGCCGACAAGCAGAAGAACGGCATCAAGGTGAACTTCAAGATCCGCCACAACATCGAGGACGGCAGCGTGCAGCTCGCCGACCACTACCAGCAGAACACCCCCATCGGCGACGGCCCCGTGCTGCTGCCCGA
>S-443_Coccidia_Sarcocystiscruzi_consensus
AGTTGGATGTCTGCTGAAAGCAGTNGGNCCCCNNCCCNATTTGTAGGGTGTGCACTTGATGAATTCTGGCATCTATGTCCCAATRgtATRTGAYGGTGtataTAgTAtYcYTGgcgaaWGtataTWYtAttatMCCWTccgTWTATTGGGATAATACYGTTACTTTGAGAAAATTAGAGTGTTTGAAGCAGGCTAATTGCCTTGAATACTGCAGCATGGAATAACAATATAGGATTTCGGTTCTATTTTGTTGGTTTCTAGGACTGAAATAATGATTAATAGGGACAGTTGGGGGCATTCGTATTTAA

Download FASTA file

RESULTS SUMMARY - Based on abricate results
SAMPLEID PATHOGEN RESULT QC.STATUS
S-615 BVDv-Type-1 Negative OK
S-615 BVDv-Type-2 Negative OK
S-615 Bacillus licheniformis Negative OK
S-615 Bovine herpesvirus type-1 Negative OK
S-615 BVDv Negative OK
S-615 Campylobacter fetus Positive OK
S-615 Campylobacter fetus subsp. venerealis Positive OK
S-615 Campylobacter jejuni subsp. jejuni Negative OK
S-615 Chlamydia abortus Negative OK
S-615 Coxiella burnetii Negative OK
S-615 Internal amplification control Positive OK
S-615 Leptospira borgpetersenii serovar. Hardjo Negative OK
S-615 Leptospira interrogans serovar. Copenhageni Negative OK
S-615 Leptospira kirschneri Negative OK
S-615 Listeria monocytogenes Negative OK
S-615 Mycoplasma bovis Negative OK
S-615 Neospora caninum Negative OK
S-615 Sarcocystis bovini Negative OK
S-615 Sarcocystis cruzi Negative OK
S-615 Sarcocystis hirsuta Negative OK
S-615 Toxoplasma gondii Negative OK
S-615 Tritrichomonas foetus Negative OK
S-615 Trueperella pyogenes Negative OK
S-615 Ureaplasma diversum Negative OK
NO. OF MAPPED READS. Generated using minimap2 and samtools
AMPLICON MAPPED_READS
CampylobacterfetusMLST-aspA 5172
CampylobacterfetusMLST-glnA 5993
CampylobacterfetusMLST-gltA 8172
CampylobacterfetusMLST-glyA 909
CampylobacterfetusMLST-pgm 3586
CampylobacterfetusMLST-tkt 8253
CampylobacterfetusMLST-uncA 29151
CFF_nahE 1987
CFV_parA 16118
IC-EGFP 11506
Consensus compared to reference database. Generated using abricate and custom database
SEQUENCE GENE %COVERAGE %IDENTITY DATABASE REFERENCE
S-615_CFF_nahE hydratase-aldolase_nahE 100 100 Bovreproseq Campylobacter_fetus
S-615_CFV_parA parA-partitioning_protein_A 100 100 Bovreproseq Campylobacter_fetus_subsp._venerealis
S-615_CampylobacterfetusMLST-aspA aspA-aspartase_A 100 100 Bovreproseq Campylobacter_fetus
S-615_CampylobacterfetusMLST-glnA glnA-glutamine_synthetase 100 100 Bovreproseq Campylobacter_fetus
S-615_CampylobacterfetusMLST-gltA gltA-citrate_synthase 100 100 Bovreproseq Campylobacter_fetus
S-615_CampylobacterfetusMLST-glyA glyA-serine_hydroxymethyltransferase 100 100 Bovreproseq Campylobacter_fetus
S-615_CampylobacterfetusMLST-pgm pgm-phosphoglucomutase 100 100 Bovreproseq Campylobacter_fetus
S-615_CampylobacterfetusMLST-tkt tkt-transketolase 100 100 Bovreproseq Campylobacter_fetus
S-615_CampylobacterfetusMLST-uncA uncA-ATP_synthase_alpha_subunit 100 100 Bovreproseq Campylobacter_fetus
S-615_IC-EGFP IC-EGFP 100 100 Bovreproseq Internal_amplification_control
MLST tool from github (https://github.com/tseemann/mlst). Scans contig files against traditional PubMLST typing schemes
FILE ST ORGANISM
S-615_medaka_consensus.fasta 4 Campylobacter fetus. venerealis 
>S-615_IC-EGFP_consensus
CAGCGTGTCCGGCGAGGGCGAGGGCGATGCCACCTACGGCAAGCTGACCCTGAAGTTCATCTGCACCACCGGCAAGCTGCCCGTGCCCTGGCCCACCCTCGTGACCACCCTGACCTACGGCGTGCAGTGCTTCAGCCGCTACCCCGACCACATGAAGCAGCACGACTTCTTCAAGTCCGCCATGCCCGAAGGCTACGTCCAGGAGCGCACCATCTTCTTCAAGGACGACGGCAACTACAAGACCCGCGCCGAGGTGAAGTTCGAGGGCGACACCCTGGTGAACCGCATCGAGCTGAAGGGCATCGACTTCAAGGAGGACGGCAACATCCTGGGGCACAAGCTGGAGTACAACTACAACAGCCACAACGTCTATATCATGGCCGACAAGCAGAAGAACGGCATCAAGGTGAACTTCAAGATCCGCCACAACATCGAGGACGGCAGCGTGCAGCTCGCCGACCACTACCAGCAGAACACCCCCATCGGCGACGGCCCCGTGCTGCTGCCCGA
>S-615_CFV_parA_consensus
TTGCGGTTGGATTATAAATTTTAGCTTGGTTGAAAACTAAAATCATCTTATTTAATACCGCAATATCAAGATCGCTTGGGATAACTGGGAT
>S-615_CampylobacterfetusMLST-glnA_consensus
TTGGCAGCCGATTCATAAATCAGATATGATGCTAAAACCAGATGTAGAAACTGCGTTTTTAGATCCTTTTACTGCAGATACGACTATTATAGTAATATGTGATGTTTATGACATATACAAAGGTGAATTATATGAAAAATGTCCTAGAAGTATAGCAAAAAAGGCATCGCAATATCTAAGAGATAGCGGTGTAGGAGACGTAGCTTACTTTGGACCTGAAAATGAGTTTTTTGTATTTGACAATGTTCGCATTATAGATAAACCAAATTGCGCTATGTATGAAGTAGATACGGAAGAAGGCGAGTGGAATGATGGTAAAGAGTATACAGATGGATACAATACGGGTCACAGACCACGCACCAAAGGTGGATATTTTCCAGTTCAACCAGTCGATAGCATGGTGGATCTAAGAGCTGAAATGGTAAATGTACTTGAACAAGTAGGACTTGAAACTTTTGTGGTTCATCATGAAGTTGCTCAAGGACAAGGCGAAATAGGCGTCAAATTCGGCACACTTGTAGAGGCTGCGGATAATGTTCAAATTTATAAATATGTAGTAAAAATGGTAGCTCATCTAAACGGTAAAACAGCTACATTTATGCCAAAACCG
>S-615_CampylobacterfetusMLST-uncA_consensus
GAACTGAGCAAAAGCTTGAAGTTCGCGATACTGAGCAAGATCAAGCCTTAGTGTTCCAGAAACTTTTTTAATAGCTTTTATCTGGGCTGATCCGCCGACACGACTAACAGACAAACCAACGTTAATAGCAGGACGAATACCTGAGTTAAACAAGTCGCTTTCCAAGAAAATTTGACCATCAGTTATAGAAATAACATTTGTAGGAATATACGCTGAAACGTCACCTGCTTGAGTCTCGATAATAGGTAGAGCCGTAAGACTTCCCGCTCCTAGTTTATCACTTAGCTTACTAGCTCTCTCAAGCAGTCTTGAGTGCAGATAGAAAACATCTCCTGGATATGCTTCACGACCCGGCGGTCTTCTTAAAATCAATGACATTTCACGGTAAGCTACAGCGTGCTTGCTTAGATCATCATAAATAATAAGAGCATGGCGTGAGTTATCACGGAAATATTCACCCATTGTTACACCTGCATATGGAGCAAGATATTGTAACGCCGGAGCATCGCTTGCACTTGCATTAACTACTATAGTATA
>S-615_CampylobacterfetusMLST-gltA_consensus
AAAATAAACTTTATCTTGATGTAGTATATTTACTATTTAACAAACACCTGCCAAGCCAAGAGGAGCTGGAGCTATTTAGACGCGAGTTAAAAGAGAGAAGCTTTTTAAATGAAAAAATGATTAGATTATTTGACTGTTTTCCCGATAAAGCTCATCCTATGGCCGTTTTACAAGCAAGCGTAGCTACCATGAGTGCATACTATAAAAGAGATATGAATTTTGATGATATGAATGATTATATGGAGCTTGCAAAACGTTTAGTGGCAAAAATTCCTACATTTATAGCGTTTTATTATCGTCATGTTAGAGGATTTCCTGTAATATATCCGAATTTAGATCGCGGATTTACAGAAAATTTCTTATATATGCTAAGAGCTTTTCCTCACGATAAGGTAGATTTAAAACCTATAGAAGTCAAGGCTTTTGATACTGTTTTGATGCTTCACGCTGATCATGAACAAAATGCTTCAACTACTACAGTTAGAA
>S-615_CampylobacterfetusMLST-aspA_consensus
TTTAAAACTTTTGCTATCATGCTTGGCGAAGATATCGACCGTGTAAGAGAAGCTAGAAACTTAGTACGCGAGATAAACCTAGGCGGAACAGCTATCGGTACAGGTATCAACTCTCACCCAGACTATCCAAAAGTAGTCGAGACAAAACTTCAAGAAGTAACAAAACGTCCATTCATCACTGCTGGTAACCTTATAGAAGCTACTCAAGACACAGGCGCTTATGTTCAAATTTCAGGCGTTTTAAAAAGAGTTAGTACAAAACTAAGCAAAATTTGTAATGACTTAAGACTTTTAAGCAGCGGCCCAAGATGCGGACTAAACGAGATAAACTTACCAAAAATGCAACCGGGCTCAAGCATTATGCCAGGCAAAGTAAATCCTGTTATCCCTGAAGTAGTAAATCAAGTTTGTTTCGCAGTTATCGGTAATGACGTAACTGTAACTCTAGCTAGCGAAGGCGGACAACTTCAACTAAACGTATTTGAACCAGTTATCGCTTATAGTCTGTTTAACTCTATCGCAATGCTTAAAAAA
>S-615_CampylobacterfetusMLST-tkt_consensus
TGGTCATGCAAGTAGCTTGGTTTATAGTTATTTATATCTTTGTGGTTATGACGTTAGTTTGGATGATTTGAAAAAATTTAGACAACTTCACTCTAAAACTCCCGGACATCCCGAGATAGAAACCCCGGGAGTAGAGATAGCAACTGGACCATTAGGACAAGGAGTGGCAAATGCTGTAGGTTTTGCCATGGCGGCAAAAAGCGCTTCAAATTTACTTGGAAATGAGATTATAAATCATAAAGTATATTGTCTGTGCGGCGATGGAGATCTAGAAGAAGGTATCAGTTATGAAGCTTGTGCTTTGGCTGGAAAACACTCTTTAGATAATTTAGTGATTATATATGATAGCAATAATATCACGATAGAGGGCGATACTAGTATAGCGTGGTGTGAAGATGTAAAAGTACGTTTTGAAGCGGCTGGATTTGAAGTTGCGCGGATAGATGGACATAATTATGATGAGATTGAATTTGCACTTTGCGAAGCAGATACGAAAGAAAAACCTTATCTTATTATCGCAAGTACAAAGATTGCTAAAGGCGC
>S-615_CFF_nahE_consensus
AACTTTGAGATAATATTTGAAAATTTATTAATGATAATAGTGATTTTGGTCGATGTTATGGTGATCAAAATAGCTGTTGTATATGCACTTTTAGCAACTTATCTTaAAAAAAGAGTAGCCATAAAAACAGCTCTTAGTATATGTCAGATTGGCGAGTTCGCTTTAGCTATTTTTGCTCTTTTAAACGTAAATAATATGTTAAATTCAGAAACTTCTCAAATTTTAACCGCGGTTGTAATTATATCTATGGTAGCTACTCCGTTGATCTTaAAAAACATCGGACATTTAGCCGACAGACTAGAAGAAGAGAGCGAAATACCTGAGTT
>S-615_CampylobacterfetusMLST-pgm_consensus
TTTTCTATAATTTTCAAATTTGAAAGTTTTTGTGGATATGCTTTAATACTCCCGAATATCTCGCTGGCTTTTTTATTTTTAGCTAAGAGACAAGCGCTTACTTGCAAAGCTGAAACAAGTCCGTCGCCGGTCTTTGAAAAATCGCTAAATATGATGTGTCCGCTCTGCTCACCGCCGAAATTTATGCCGTTTTCTTTCATCATTTCAAGAACGAATTTATCTCCGACGTTTGAACGAAGAAGCTTAATTTTGTGTTTTGCAAGATAGTCGTCAAGTGCGGCATTACTCATCACGGTGGCTACTATCTCCTTTTTATCAAGCATCTTATTTTCATCAAGATAAGTAGCCAAAACGCCGAGCAAAGCGTCTCCATCGACAACTTTTGCATTTTCATCGACAACCACAAGTCTATCGGCATCACCGTCAAAAGCAAATCCTATATCGGCTCTTAATCTTTTAACTTCTTTTGCCAAATTTTCAGGATGCAAAGCACCGCAGCCATCATTTATATTTCCGCCGTTTGGTTCATCGTTTAAAACTATTGTCTCTGCTCCAAGCTCGCTAAATACGGTCGGAGCGACTTTATAAACTGCGCCGTTT
>S-615_CampylobacterfetusMLST-glyA_consensus
CCGAGTTTTTTAGCGTTTGTCTTTACTTGCTTAGCATAAACTTTCCACTCGTCACTAAGATTATGCTTAAATCCAACTGCTTTTCCAGCAATCACGTGCATAAGCGGCCCGCCTTGAATTCCCGGAAATATAGAACTATTTATTTTTTTAGCAAATTCCTCATCATTTGTCATGATGATACCGCCTCTTGGACCTCTTAATGTTTTATGAGTAGTTGAACTTACAACGTGACAGTGAGGAAATGGATTGTTATGTTCTCCTGCTACTACAAGACCTGCTATATGAGCAACATCGGCAAATAAATATGCTCCAACGCTATCGGCTATCTCTCTAAATTTCTTAAAATCAATCTCTCTAGCATAAGCACTAGCACCGCAAACTATCATTTTAGGTTTAGTTATATTTGCTATCTCTTCTACTTTATTATAATTTATACGTCCATCAAGCTCAACACCGTAGAAAAAGCTCTCATAGTTTTTTCCAGAGCTTGAAACTTTAGAACCGTGAGTAAGGTGTCCACCATGGCTTA

Download FASTA file

RESULTS SUMMARY - Based on abricate results
SAMPLEID PATHOGEN RESULT QC.STATUS
S-805-2 BVDv-Type-1 Positive OK
S-805-2 BVDv-Type-2 Negative OK
S-805-2 Bacillus licheniformis Negative OK
S-805-2 Bovine herpesvirus type-1 Negative OK
S-805-2 BVDv Positive OK
S-805-2 Campylobacter fetus Negative OK
S-805-2 Campylobacter fetus subsp. venerealis Negative OK
S-805-2 Campylobacter jejuni subsp. jejuni Negative OK
S-805-2 Chlamydia abortus Negative OK
S-805-2 Coxiella burnetii Negative OK
S-805-2 Internal amplification control Positive OK
S-805-2 Leptospira borgpetersenii serovar. Hardjo Negative OK
S-805-2 Leptospira interrogans serovar. Copenhageni Negative OK
S-805-2 Leptospira kirschneri Negative OK
S-805-2 Listeria monocytogenes Negative OK
S-805-2 Mycoplasma bovis Negative OK
S-805-2 Neospora caninum Negative OK
S-805-2 Sarcocystis bovini Positive OK
S-805-2 Sarcocystis cruzi Negative OK
S-805-2 Sarcocystis hirsuta Negative OK
S-805-2 Toxoplasma gondii Negative OK
S-805-2 Tritrichomonas foetus Negative OK
S-805-2 Trueperella pyogenes Negative OK
S-805-2 Ureaplasma diversum Negative OK
NO. OF MAPPED READS. Generated using minimap2 and samtools
AMPLICON MAPPED_READS
BVDv_Npro 126
BVDv-1_5’UTR 21442
IC-EGFP 34208
Sarcocystis_spp 389
Coccidia_Spp. 11
Consensus compared to reference database. Generated using abricate and custom database
SEQUENCE GENE %COVERAGE %IDENTITY DATABASE REFERENCE
S-805-2_BVDv-1_5’UTR 5’UTR 98.78 90.12 Bovreproseq BVDv-Type-1
S-805-2_BVDv_Npro Npro-N-terminal_autoprotease 97.69 81.84 Bovreproseq BVDv
S-805-2_Coccidia_Spp. Coccidia-18SrRNA 99.68 88.58 Bovreproseq Aspergillus_fumigatus_isolate
S-805-2_IC-EGFP IC-EGFP 100.00 100.00 Bovreproseq Internal_amplification_control
S-805-2_Sarcocystis_spp Sarcocystis-18SrRNA 86.72 93.32 Bovreproseq Sarcocystis_bovini 
>S-805-2_IC-EGFP_consensus
CAGCGTGTCCGGCGAGGGCGAGGGCGATGCCACCTACGGCAAGCTGACCCTGAAGTTCATCTGCACCACCGGCAAGCTGCCCGTGCCCTGGCCCACCCTCGTGACCACCCTGACCTACGGCGTGCAGTGCTTCAGCCGCTACCCCGACCACATGAAGCAGCACGACTTCTTCAAGTCCGCCATGCCCGAAGGCTACGTCCAGGAGCGCACCATCTTCTTCAAGGACGACGGCAACTACAAGACCCGCGCCGAGGTGAAGTTCGAGGGCGACACCCTGGTGAACCGCATCGAGCTGAAGGGCATCGACTTCAAGGAGGACGGCAACATCCTGGGGCACAAGCTGGAGTACAACTACAACAGCCACAACGTCTATATCATGGCCGACAAGCAGAAGAACGGCATCAAGGTGAACTTCAAGATCCGCCACAACATCGAGGACGGCAGCGTGCAGCTCGCCGACCACTACCAGCAGAACACCCCCATCGGCGACGGCCCCGTGCTGCTGCCCGA
>S-805-2_Sarcocystis_spp_consensus
TTACTTTGAGAAAATTAGAGTGTTTGAAGCAGGCAATTGCCTTGAATACTGCAGCATGGAATAACAACATAGGATTTCGGTTCTATTTTGTTGGTTTCAGGACTGAAATAATGATTAATAGGGACAGTCGGGGGCATTCGTATTTAACTGTCAGAGGTGAAATTCTTAGATTTGTAAAGACGAACAACTGCGAAAGCATTTGCCAAGGATGTTTTCATTAATCAAGAACGAAAGTTAGGGGCTCGAAGACGATCAGATACCGTCCTAGTCTCAACCATAAACGATGCCGACCAGGGATCGGCGGATGTTGCTTATAGGACTCCGCCGGCACCTTATGAGAAATCAAAGTTTTTGGGTTCCGGGGGGAGTATGGTCGCAAGGCTGAAACTTAAAGGAATTGACGGAAGGGCACCACCAGGAGTGGAGCCTGCGGCTTAATTTGACTCAACACGGGGAAACTTACCAGGTCCAGACATAGTAAGGATTGACAGACTGAGAGCTCTT
>S-805-2_BVDv_Npro_consensus
GGCACATGGAGTTGATCACAAATGAACTTTTATACAAAACATACAAACAAAAACCCACTGGAGTGGAGGAACCAGTATACGACCAAGCTGGTAACCCTTTGTTTGGAGAAAGAGGAGAGATTCATCCGCAGTCAACGCTAAAACTGCCACATAAAAGAGGGGCACGCGAAGTACCCACCAATTTGGCTTCTTTACCAAAAAGAGGTGACTGCAGGTCGGGTAACAGCAAGGGGCCTGTGAGTGGAATCTACTTAAAACCAGGGCCGTTATTCTACCAGGATTATAAAGGACCTGTCTATCATAGAGCCCCATTGGAGTTTTTTGAAGAAGCGTCTATGTGTGAGATAACCAAAAGAATCGGGAGAGTAACTGGTAGTGACAGCAAATTA
>S-805-2_Coccidia_Spp._consensus
GTTGTTGCAGTTAAAAAGCTSGTAGTTGAAACTTGGGcYCNGGCTGGCAGGTCCGCCTCACCGCGTGTACTTgccggccGNNCGGNCKGGCctTTCCTTCTGGAGAACCTCATGCCCTTCACTGGGtgGTGTKggKKgggAACCAGGACTTTTACTTTGAAAAAATTAGAGTGTTCAAAGCAGGCCTTTGCTCGAATACGTTAGCATGGAATAATAGAATAGGACGTGCGGTCCTATTTTGTTGGTTTCTAGGACCGCCGTAATGATTAATAGGGACAGTNGGGGGCATCAGTATTCAANTGTCAGAGGTGAAATTCTTAGAT
>S-805-2_BVDv-1_5'UTR_consensus
AAAATAAGGGGGGTAGCAACAGTGGTGAGTTTGTTGGATGGCTGAAGCCCTGAGTACAGGGTAGTCGTCAGTGGTTCGACGCTTTGGAGAATGAGCCTCGAGATGCCACGTGGACGAGGGCATGCCCACAGCACATCTTAGCCTGGACGGGGGTCGTTCAGGTGAAAACGGTTTAATCAACCGCTACGAATACAGCCTGATAGGGTGCTGCAGAGGCCCACTGTATTGCTACTAAAAATCTCTG

Download FASTA file

RESULTS SUMMARY - Based on abricate results
SAMPLEID PATHOGEN RESULT QC.STATUS
S-807-4 BVDv-Type-1 Negative OK
S-807-4 BVDv-Type-2 Negative OK
S-807-4 Bacillus licheniformis Negative OK
S-807-4 Bovine herpesvirus type-1 Negative OK
S-807-4 BVDv Negative OK
S-807-4 Campylobacter fetus Negative OK
S-807-4 Campylobacter fetus subsp. venerealis Negative OK
S-807-4 Campylobacter jejuni subsp. jejuni Negative OK
S-807-4 Chlamydia abortus Negative OK
S-807-4 Coxiella burnetii Positive OK
S-807-4 Internal amplification control Positive OK
S-807-4 Leptospira borgpetersenii serovar. Hardjo Negative OK
S-807-4 Leptospira interrogans serovar. Copenhageni Negative OK
S-807-4 Leptospira kirschneri Negative OK
S-807-4 Listeria monocytogenes Negative OK
S-807-4 Mycoplasma bovis Negative OK
S-807-4 Neospora caninum Negative OK
S-807-4 Sarcocystis bovini Negative OK
S-807-4 Sarcocystis cruzi Negative OK
S-807-4 Sarcocystis hirsuta Negative OK
S-807-4 Toxoplasma gondii Negative OK
S-807-4 Tritrichomonas foetus Negative OK
S-807-4 Trueperella pyogenes Negative OK
S-807-4 Ureaplasma diversum Negative OK
NO. OF MAPPED READS. Generated using minimap2 and samtools
AMPLICON MAPPED_READS
Coxiella_burnetti_COM1 51
Coxiella_burnetti_Trans-1 7666
IC-EGFP 5190
Sarcocystis_spp 42
Consensus compared to reference database. Generated using abricate and custom database
SEQUENCE GENE %COVERAGE %IDENTITY DATABASE REFERENCE
S-807-4_Coxiella_burnetti_COM1 com1-Outer_membrane_protein 100.00 99.85 Bovreproseq Coxiella_burnetii
S-807-4_Coxiella_burnetti_Trans-1 Transposon-like_element 99.69 99.53 Bovreproseq Coxiella_burnetii
S-807-4_IC-EGFP IC-EGFP 100.00 100.00 Bovreproseq Internal_amplification_control
S-807-4_Sarcocystis_spp Sarcocystis-18SrRNA 100.00 100.00 Bovreproseq Oryza_glumipatula 
>S-807-4_IC-EGFP_consensus
CAGCGTGTCCGGCGAGGGCGAGGGCGATGCCACCTACGGCAAGCTGACCCTGAAGTTCATCTGCACCACCGGCAAGCTGCCCGTGCCCTGGCCCACCCTCGTGACCACCCTGACCTACGGCGTGCAGTGCTTCAGCCGCTACCCCGACCACATGAAGCAGCACGACTTCTTCAAGTCCGCCATGCCCGAAGGCTACGTCCAGGAGCGCACCATCTTCTTCAAGGACGACGGCAACTACAAGACCCGCGCCGAGGTGAAGTTCGAGGGCGACACCCTGGTGAACCGCATCGAGCTGAAGGGCATCGACTTCAAGGAGGACGGCAACATCCTGGGGCACAAGCTGGAGTACAACTACAACAGCCACAACGTCTATATCATGGCCGACAAGCAGAAGAACGGCATCAAGGTGAACTTCAAGATCCGCCACAACATCGAGGACGGCAGCGTGCAGCTCGCCGACCACTACCAGCAGAACACCCCCATCGGCGACGGCCCCGTGCTGCTGCCCGA
>S-807-4_Coxiella_burnetti_COM1_consensus
ACTGCAGGCGTGGCGATAGCCGCCCCCTCTCAATCCAGTTTTTCTCCTCAACAAGTCAAAGACATACAAAGCATCGTCCACCATTATTTAGTCAACCACCCAGAAGTTTTAGTAGAAGCATCCCAAGCATTGCAAAAAAAGACAGAAGCGCAACAAGAAGAACACGCTCAACAAGCAATTAAAGAAAATGCAAAGAAATTATTTAACGACCCTGCATCACCAGTGGCAGGCAATCCTCATGGCAATGTTACATTGGTTGAATTTTTCGATTATCAATGTGGCCATTGCAAAGCCATGAATTCTGTTATTCAAGCTATCGTGAAACAAAATAAAAACCTCCGCGTTGTCTTCAAAGAACTGCCCATTTTTGGCGGCCAATCGCAATACGCTGCCAAAGTATCATTAGCAGCCGCTAAACAAGGAAAATATTATGCTTTCCACGACGCGCTGCTCAGTGTCGACGGCCAATTATCAGAACAAATCACCCTTCAAACCGCAGAAAAAGTAGGATTAAATGTTGCTCAGCTCAAAAAAGACATGGATAATCCTGCTATCCAAAAACAACTGCGTGATAACTTCCAATTAGCTCAATCGTTACAGCTAGCAGGCACCCCGACGTTCGTCATTGGTAATAAAGCGTTAACCAAATTCGGTTTTATACCCGGCGCCACCTCACAACAAAACCTTCA
>S-807-4_Sarcocystis_spp_consensus
GTTACTTTGAAGAAATTAGAGTGCTCAAAGCAAGCCATCGCTCTGGATACATTAGCATGGGATAACATCATAGGATTCCGGTCCTATTGTGTTGGCCTTCGGGATCGGAGTAATGATTAATAGGGACAGTCGGGGGCATTCGTATTTCATAGTCAGAGGTGAAATTCTTGGATTTATGAAAGACGAACAACTGCGAAAGCATTTGCCAAGGATGTTTTCATTAATCAAGAACGAAAGTTGGGGGCTCGAAGACGATCAGATACCGTCCTAGTCTCAACCATAAACGATGCCGACCAGGGATCGGCGGATGTTGCTTATAGGACTCCGCCGGCACCTTATGAGAAATCAAAGTCTTTGGGTTCCGGGGGGAGTATGGTCGCAAGGCTGAAACTTAAAGGAATTGACGGAAGGGCACCACCAGGCGTGGAGCCTGCGGCTTAATTTGACTCAACACGGGGAAACTTACCAGGTCCAGACATAGCAAGGATTGACAGACTGAGAGCTCTT
>S-807-4_Coxiella_burnetti_Trans-1_consensus
TTAAGGTGGGCTGCGTGGTGATGGAAGCGTGTGGAGGAGCGAACCATTGGTATCGGACGTTTATGGGGATGGGTATCTCAACGCAGTTGATCAGTCCGCAGCACGTCAAACCGTATGTCAAAAGTAACAAGAATGATCGTAACGATGCGCAGGCGATAGCTGAAGCGGCTTCCCGCGCCTCGATGCGGTTTGTGCGGGGTAAAACGGTGGAACAACAAGACGTTCAAGCGCTGTTAAAGATACGCGATCGTTTAGTCAAAAGCCGCACGGCGCTGATCAATGAGATTCGGGGGTTGTTGCAAGAATACGGACTCACGATGGCGCGTGGTGCCAAGCGATTTTATGAAGAGCTCCCGTTGATTTTAGCGAGCGAAGCGGTGGGATTAACACCGCGGATGAAACGGGTGTTGAATTGTTTGTATACCGAATTGTTGAACCGGGACGAAGCGATTGGTGATTACGAGGAGGAATTAAAAGCGGTGGCAAAAGCCAATGAGGATTGTCAACGGGTACAGAGCATCCCGGGGGTGGGTTATTTAACGGCGCTGTCGGTTTATGCGAGCGTGGGTGACATTCATCAATTTCATCGTTCCCGGCAGTTGTCGGCGTTTATTGGGTTGGTCCCTCGACAACATTCGAGGG

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RESULTS SUMMARY - Based on abricate results
SAMPLEID PATHOGEN RESULT QC.STATUS
S-907-1 BVDv-Type-1 Negative OK
S-907-1 BVDv-Type-2 Negative OK
S-907-1 Bacillus licheniformis Negative OK
S-907-1 Bovine herpesvirus type-1 Negative OK
S-907-1 BVDv Negative OK
S-907-1 Campylobacter fetus Positive OK
S-907-1 Campylobacter fetus subsp. venerealis Negative OK
S-907-1 Campylobacter jejuni subsp. jejuni Negative OK
S-907-1 Chlamydia abortus Negative OK
S-907-1 Coxiella burnetii Negative OK
S-907-1 Internal amplification control Positive OK
S-907-1 Leptospira borgpetersenii serovar. Hardjo Negative OK
S-907-1 Leptospira interrogans serovar. Copenhageni Negative OK
S-907-1 Leptospira kirschneri Negative OK
S-907-1 Listeria monocytogenes Negative OK
S-907-1 Mycoplasma bovis Negative OK
S-907-1 Neospora caninum Negative OK
S-907-1 Sarcocystis bovini Negative OK
S-907-1 Sarcocystis cruzi Negative OK
S-907-1 Sarcocystis hirsuta Negative OK
S-907-1 Toxoplasma gondii Negative OK
S-907-1 Tritrichomonas foetus Negative OK
S-907-1 Trueperella pyogenes Negative OK
S-907-1 Ureaplasma diversum Negative OK
NO. OF MAPPED READS. Generated using minimap2 and samtools
AMPLICON MAPPED_READS
CampylobacterfetusMLST-aspA 10332
CampylobacterfetusMLST-glnA 13154
CampylobacterfetusMLST-gltA 15633
CampylobacterfetusMLST-glyA 3763
CampylobacterfetusMLST-pgm 8812
CampylobacterfetusMLST-tkt 7938
CampylobacterfetusMLST-uncA 87447
CFF_nahE 5915
IC-EGFP 96481
Consensus compared to reference database. Generated using abricate and custom database
SEQUENCE GENE %COVERAGE %IDENTITY DATABASE REFERENCE
S-907-1_CFF_nahE hydratase-aldolase_nahE 100 99.39 Bovreproseq Campylobacter_fetus
S-907-1_CampylobacterfetusMLST-aspA aspA-aspartase_A 100 100.00 Bovreproseq Campylobacter_fetus
S-907-1_CampylobacterfetusMLST-glnA glnA-glutamine_synthetase 100 100.00 Bovreproseq Campylobacter_fetus
S-907-1_CampylobacterfetusMLST-gltA gltA-citrate_synthase 100 100.00 Bovreproseq Campylobacter_fetus
S-907-1_CampylobacterfetusMLST-glyA glyA-serine_hydroxymethyltransferase 100 100.00 Bovreproseq Campylobacter_fetus
S-907-1_CampylobacterfetusMLST-pgm pgm-phosphoglucomutase 100 100.00 Bovreproseq Campylobacter_fetus
S-907-1_CampylobacterfetusMLST-tkt tkt-transketolase 100 99.82 Bovreproseq Campylobacter_fetus
S-907-1_CampylobacterfetusMLST-uncA uncA-ATP_synthase_alpha_subunit 100 99.63 Bovreproseq Campylobacter_fetus
S-907-1_IC-EGFP IC-EGFP 100 100.00 Bovreproseq Internal_amplification_control
MLST tool from github (https://github.com/tseemann/mlst). Scans contig files against traditional PubMLST typing schemes
FILE ST ORGANISM
S-907-1_medaka_consensus.fasta 2 Campylobacter fetus. fetus 
>S-907-1_IC-EGFP_consensus
CAGCGTGTCCGGCGAGGGCGAGGGCGATGCCACCTACGGCAAGCTGACCCTGAAGTTCATCTGCACCACCGGCAAGCTGCCCGTGCCCTGGCCCACCCTCGTGACCACCCTGACCTACGGCGTGCAGTGCTTCAGCCGCTACCCCGACCACATGAAGCAGCACGACTTCTTCAAGTCCGCCATGCCCGAAGGCTACGTCCAGGAGCGCACCATCTTCTTCAAGGACGACGGCAACTACAAGACCCGCGCCGAGGTGAAGTTCGAGGGCGACACCCTGGTGAACCGCATCGAGCTGAAGGGCATCGACTTCAAGGAGGACGGCAACATCCTGGGGCACAAGCTGGAGTACAACTACAACAGCCACAACGTCTATATCATGGCCGACAAGCAGAAGAACGGCATCAAGGTGAACTTCAAGATCCGCCACAACATCGAGGACGGCAGCGTGCAGCTCGCCGACCACTACCAGCAGAACACCCCCATCGGCGACGGCCCCGTGCTGCTGCCCGA
>S-907-1_CampylobacterfetusMLST-aspA_consensus
TTTAAAACTTTTGCTATCATGCTTGGCGAAGATATCGACCGTGTAAGAGAAGCTAGAAACTTAGTACGCGAGATAAACCTAGGCGGAACAGCTATCGGTACAGGTATCAACTCTCACCCAGACTATCCAAAAGTAGTCGAGACAAAACTTCAAGAAGTAACAAAACGTCCATTCATCACTGCTGGTAACCTTATAGAAGCTACTCAAGACACAGGCGCTTATGTTCAAATTTCAGGCGTTTTAAAAAGAGTTAGTACAAAACTAAGCAAAATTTGTAATGACTTAAGACTTTTAAGCAGCGGCCCAAGATGCGGACTAAACGAGATAAACTTACCAAAAATGCAACCGGGCTCAAGCATTATGCCAGGCAAAGTAAATCCTGTTATCCCTGAAGTAGTAAATCAAGTTTGTTTCGCAGTTATCGGTAATGACGTAACTGTAACTCTAGCTAGCGAAGGCGGACAACTTCAACTAAACGTATTTGAACCAGTTATCGCTTATAGTCTGTTTAACTCTATCGCAATGCTTaAAAAAA
>S-907-1_CampylobacterfetusMLST-glnA_consensus
TTGGCAGCCGATTCATAAATCAGATATGATGCTAAAACCAGATGTAGAAACTGCGTTTTTAGATCCTTTTACTGCAGATACGACTATTATAGTAATATGTGATGTTTATGACATATACAAAGGTGAATTATATGAAAAATGTCCTAGAAGTATAGCAAAAAAGGCATCGCAATATCTAAGAGATAGCGGTGTAGGAGACGTAGCTTACTTTGGACCTGAAAATGAGTTTTTTGTATTTGACAATGTTCGCATTATAGATAAACCAAATTGCGCTATGTATGAAGTAGATACGGAAGAAGGCGAGTGGAATGATGGTAAAGAGTATACAGATGGATACAATACGGGTCACAGACCACGCACCAAAGGTGGATATTTTCCAGTTCAACCAGTCGATAGCATGGTGGATCTAAGAGCTGAAATGGTAAATGTACTTGAACAAGTAGGACTTGAAACTTTTGTGGTTCATCATGAAGTTGCTCAAGGACAAGGCGAAATAGGCGTCAAATTCGGCACACTTGTAGAGGCTGCGGATAATGTTCAAATTTATAAATATGTAGTAAAAATGGTAGCTCATCTAAACGGTAAAACAGCTACATTTATGCCAAAACCG
>S-907-1_CampylobacterfetusMLST-gltA_consensus
AAAATAAACTTTATCTTGATGTAGTATATTTACTATTTAACAAACACCTGCCAAGCCAAGAGGAGCTGGAGCTATTTAGACGCGAGTTAAAAGAGAGAAGCTTTTTAAATGAAAAAATGATTAGATTATTTGACTGTTTTCCCGATAAAGCTCATCCTATGGCCGTTTTACAAGCAAGCGTAGCTACCATGAGTGCATACTATAAAAGAGATATGAATTTTGATGATATGAATGATTATATGGAGCTTGCAAAACGTTTAGTGGCAAAAATTCCTACATTTATAGCGTTTTATTATCGTCATGTTAGAGGATTTCCTGTAATATATCCGAATTTAGATCGCGGATTTACAGAAAATTTCTTATATATGCTAAGAGCTTTTCCTCACGATAAGGTAGATTTAAAACCTATAGAAGTCAAGGCTTTTGATACTGTTTTGATGCTTCACGCTGATCATGAACAAAATGCTTCAACTACTACAGTTAGAA
>S-907-1_CampylobacterfetusMLST-tkt_consensus
TGGTCATGCAAGTAGCTTGGTTTATAGTTATTTATATCTTTGTGGTTATGACGTTAGTTTGGATGATTTGAAAAAATTTAGACAACTTCACTCTAAAACTCCCGGACATCCCGAGATAGAAACCCCGGGAGTAGAGATAGCAACTGGACCATTAGGACAAGGAGTGGCAAATGCTGTAGGTTTTGCCATGGCGGCAAAAAGCGCTTCAAATTTACTTGGAAATGAGATTATAAATCATAAAGTATATTGTCTGTGCGGCGATGGAGATCTAGAAGAAGGTATCAGTTATGAAGCTTGTGCTTTGGCTGGAAAACACTCTTTAGATAATTTAGTGATTATATATGATAGCAATAATATCACGATAGAGGGCGATACTAGTATAGCGTGGTGTGAAGATGTAAAAGTACGTTTTGAAGCGGCTGGATTTGAGGTTGCGCGGATAGATGGACATAATTATGATGAGATTGAATTTGCACTTTGCGAAGCAGATACGAAAGAAAAACCTTATCTTATTATCGCAAGTACAAAGATTGCTAAAGGCGC
>S-907-1_CampylobacterfetusMLST-pgm_consensus
TTTTCTATAATTTTCAAATTTGAAAGTTTTTGTGGATATGCTTTAATACTCCCGAATATCTCGCTGGCTTTTTTATTTTTAGCTAAGAGACAAGCGCTTACTTGCAAAGCTGAAACAAGTCCGTCGCCGGTCTTTGAAAAATCGCTAAATATGATGTGTCCGCTCTGCTCACCGCCGAAATTTATGCCGTTTTCTTTCATCATTTCAAGAACGAATTTATCTCCGACGTTTGAACGAAGAAGCTTAATTTTGTGTTTTGCAAGATAGTCGTCAAGTGCGGCATTACTCATCACGGTGGCTACTATCTCCTTTTTATCAAGCATCTTATTTTCATCAAGATAAGTAGCCAAAACGCCGAGCAAAGCGTCTCCATCGACAACTTTTGCATTTTCATCGACAACCACAAGTCTATCGGCATCACCGTCAAAAGCAAATCCTATATCGGCTCTTAATCTTTTAACTTCTTTTGCCAAATTTTCAGGATGCAAAGCACCGCAGCCATCATTTATATTTCCGCCGTTTGGTTCATCGTTTAAAACTATTGTCTCTGCTCCAAGCTCGCTAAATACGGTCGGAGCGACTTTATAAACTGCGCCGTTT
>S-907-1_CFF_nahE_consensus
AACTTTGAGATAATATTTGAAAATTTATTAATGATAATAGTGATTTTGGTCGATGTTATGGTGATCAAAATAGCTGTTGTATATGCACTTTTAGCAACTTATCTTaAAAAAAGAGTAGCCATAAAAACAGCTCTTAGTATATGTCAGATTGGCGAGTTCGCTTTAGCTATTTTTGCTCTTTTAAACGTAAATAATATGTTAAATTCAGAAACTTCTCAAATTTTAACCGCGGTTGTAATTATATCTATGGTAGCTACTCCGTTTATATTAAAAAACATCGGACATTTAGCCGACAGACTAGAAGAAGAGAGCGAAATACCTGAGTT
>S-907-1_CampylobacterfetusMLST-glyA_consensus
CCGAGTTTTTTAGCGTTTGTCTTTACTTGCTTAGCATAAACTTTCCACTCGTCACTAAGATTATGCTTAAATCCAACTGCTTTTCCAGCAATCACGTGCATAAGCGGCCCGCCTTGAATTCCCGGAAATATAGAACTATTTATTTTTTTAGCAAATTCCTCATCATTTGTCATGATGATACCGCCTCTTGGACCTCTTAATGTTTTATGAGTAGTTGAACTTACAACGTGACAGTGAGGAAATGGATTGTTATGTTCTCCTGCTACTACAAGACCTGCTATATGAGCAACATCGGCAAATAAATATGCTCCAACGCTATCGGCTATCTCTCTAAATTTCTTAAAATCAATCTCTCTAGCATAAGCACTAGCACCGCAAACTATCATTTTAGGTTTAGTTATATTTGCTATCTCTTCTACTTTATTATAATTTATACGTCCATCAAGCTCAACACCGTAGAAAAAGCTCTCATAGTTTTTTCCAGAGCTTGAAACTTTAGAACCGTGAGTAAGGTGTCCACCATGGCTTA
>S-907-1_CampylobacterfetusMLST-uncA_consensus
GAACTGAGCAAAAGCTTGAAGTTCGCGATACTGAGCAAGATCAAGCCTTAGTGTTCCAGAAACTTTTTTGATAGCTTTTATCTGGGCTGATCCGCCGACACGACTAACAGACAAACCAACGTTAATAGCAGGACGAATACCTGAGTTAAACAAGTCGCTTTCCAAGAAAATTTGACCATCAGTTATAGAAATAACATTTGTAGGAATATACGCTGAAACGTCACCTGCTTGAGTCTCGATAATAGGTAGAGCCGTAAGACTTCCCGCTCCTAGTTTATCACTTAGCTTACTAGCTCTCTCAAGCAGTCTTGAGTGCAGATAGAAAACATCTCCTGGATATGCTTCACGACCCGGCGGTCTTCTTAAAATCAATGACATTTCACGGTAAGCTACAGCGTGCTTGCTTAGATCATCATAAATAATAAGAGCATGGCGTGAGTTATCACGGAAATATTCACCCATTGTTACACCTCCATATGGAGCAAGATATTGTAACGCCGGAGCATCGCTTGCACTTGCATTAACTACTATAGTATA

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Taxonomic classification of raw reads